The notches are defined as +/-1.58*IQR/sqrt(n) and represent the 95% confidence interval for each median.
Non-overlapping notches give roughly 95% confidence that two medians differ, ie, in 19 out of 20 cases the population
medians (estimated based on the samples) are in fact different (Chambers et al., 1983).

Colour(s):

Colours in HEX format can be chosen on http://colorbrewer2.org/

Modify labels and title

Rotate sample names

X-axis label:

Y-axis label:

Boxplot title:

Boxplot subtitle:

Adjust plot size

Plot height:

Plot width:

Change font sizes

Title font size:

Axis label size:

Axis font size:

Orientation of box plots:

Vertical

Horizontal

Y-axis range (eg., '0,10'):

X-axis range (eg., '0,10'):

Change to log scale (only for data >0)

Add grid:

This application was developed with Nature Methods as described in this editorial and this
blog entry. Nature methods also dedicated a
Points of View and a Points of Significance
column to box plots. We hope that you find the BoxPlotR useful and we welcome suggestions
for additional features by our users. We would like to thank everyone who has made constructive suggestions so far. We will document the addition of new features in the News tab.

This application allows users to generate customized box plots in a number of variants based on their data. A data matrix
can be uploaded as a file or pasted into the application. Basic box plots are generated based on the data and can be modified to include
additional information. Additional features become available when checking that option. Information about sample sizes can be represented
by the width of each box where the widths are proportional to the square roots of the number of observations n. Notches can be added to the
boxes. These are defined as +/-1.58*IQR/sqrt(n) which gives roughly 95% confidence that two medians are different. It is also possible to define
the whiskers based on the ideas of Spear and Tukey. Additional options of data visualization (violin and bean plots) reveal more information
about the underlying data distribution. Plots can be labeled, customized (colors, dimensions, orientation) and exported as eps, pdf and svg files.

BoxPlotR code can be run locally via GitHub. You can also download and install it as a virtual machine (see GitHub and FAQs for details).

Further references

This application was created by the
Tyers
and
Rappsilber
labs. Please send bugs and feature requests to Michaela Spitzer (michaela.spitzer(at)gmail.com) and Jan Wildenhain (jan.wildenhain(at)gmail.com). This application uses the
shiny package from RStudio
.

This application was created by the
Tyers
and
Rappsilber
labs. Please send bugs and feature requests to Michaela Spitzer (michaela.spitzer(at)gmail.com) and Jan Wildenhain (jan.wildenhain(at)gmail.com). This application uses the
shiny package from RStudio
.

Box plot statistics

This application was created by the
Tyers
and
Rappsilber
labs. Please send bugs and feature requests to Michaela Spitzer (michaela.spitzer(at)gmail.com) and Jan Wildenhain (jan.wildenhain(at)gmail.com). This application uses the
shiny package from RStudio
.

Box plot description for figure legend:

Further information to be added to the figure legend:

This application was created by the
Tyers
and
Rappsilber
labs. Please send bugs and feature requests to Michaela Spitzer (michaela.spitzer(at)gmail.com) and Jan Wildenhain (jan.wildenhain(at)gmail.com). This application uses the
shiny package from RStudio
.

January 11, 2017

If you experience problems with this boxplot server, there is an alternative BoxPlotR mirror available at boxplot.bio.ed.ac.uk.

July 23, 2014

Upgrade to R version 3.1 and shiny-server 1.2

March 18, 2014

The user can now choose the color of the data points. There is also an additional option for data point display: data points can now be randomly jittered.
A small bug in label display was fixed. Log scales can now be used.

Q: I have trouble editing the graphic files.

A: For EPS files make sure to 'ungroup' all objects so they can be edited independently.
In Adobe Illustrator you will also need to use the 'release compound path' command. For PDF
files you should 'release clipping mask'. SVG import appears to have problems in Adobe Illustrator
and Corel Draw and should be avoided. EPS, PDF and SVG import all work with Inkscape http://www.inkscape.org/.

Q: I would like to install BoxPlotR as a virtual machine.

A: Please download the virtual machine from http://tyerslab.bio.ed.ac.uk/download/shiny.boxplot.7z (1.1GB).
Unzip the file using 7zip or equivalent. The virtual machine is available in the open
virtualization format (OVF) and you can use this file with vbox and
vmware player.
One easy way to use the server is to set the virtual host network environment to NAT. After importing the virtual machine you can
start the server and login as user shiny with password pk635153Y6jx89r. On the command line use the command ifconfg and record the
IP address of the virtual server. Now going back to the virtual host network environment change the advanced settings of the NAT and
activate port forwarding for the guest network ip address (shiny server) using port 80 to the host ip address using for example port 8080.
Now you should be able to access the shiny server in a browser on port 127.0.0.1:8080 or your localhost:8080.
If you are not familiar with the software packages there are detailed examples for
vbox and
vmware.